A consistent theme has dominated the discussions that take place during our yearly workshops: discovery programs are investigating compounds that lie in the Bro5 chemical space. These molecules can be peptides, macrocycles, or proteolysis targeting chimeras (PROTACs). This year, we chose to highlight physicochemical properties as they relate to PROTACs. Registration this year was at an all-time high, with a final count of 210 registrants. Most registrants came from the pharmaceutical industry (62%) followed by academia (28%).
PROTACs consist of three components: a ligand that binds to a target protein, a ligand that binds to a an E3 ubiquitin ligase, and a linker chain connecting the two. While small molecules are designed to inhibit protein activity by binding to a specific site on a target protein, PROTACs are designed to bring the protein of interest and an E3 ubiquitin ligase close enough together to form a ternary complex. This formation causes the ubiquitination of the target protein, resulting in the degradation of the target protein via the proteosome. Their mechanism of action allows them to be active within the cell for longer durations and at significantly lower concentrations than the traditional small molecule, but designing a PROTAC that can successfully enter a cell is a top challenge.
PROTACs are large compounds (MW > 1000 Da), and can fold and contort their structures based on the environment they’re in. A poll conducted at the beginning of the workshop showed a unanimous consensus that while permeability is the most important property to consider in PROTAC design, it is also the most challenging to measure experimentally due their large size, poor solubility, and tendency to stick to labware.
The presentations this year offered insight on how to measure PROTAC permeability as well as optimize it. PAMPA, MDCK, and Caco-2 were universally cited as a starting point to assess permeability in-vitro, however none of them consistently correlate with cell permeability. Lipophilicity and solubility measurements should also be considered given their impact on permeability. Stability in plasma was also mentioned, as optimizing PROTACs for permeability can negatively affect the stability of the ternary complex and reduce PROTAC function.
After 2 days of presentations from PROTAC experts and roundtable dialogue among the participants, one thing is certainly clear: research about the discovery and design of PROTACs has only just begun, and breakthroughs are made when industry and academia work together to solve common problems. Due to the lack of experimental data available for PROTACs, we are far from being able to predict their physicochemical properties, however we hope to continue to drive the discussion around the importance of considering physicochemical properties when designing them.
Workshop Speakers
